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Tropical animal health and production2021; 53(3); 334; doi: 10.1007/s11250-021-02776-2

Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers.

Abstract: We investigated the genetic diversity and population genetic structure of six morphologically distinct Ethiopian donkey populations using 12 equine microsatellite markers. The donkey populations were Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI). Blood samples were collected from 180 genetically unrelated donkeys (30 individuals per population). Population genetic diversity estimates showed that total number and mean number of observed alleles, average observed and expected heterozygosity were 94, 5.208 ± 0.0229, 0.555 ± 0.023 and 0.588 ± 0.022, respectively. Highly significant deficiency in heterozygote was detected within the overall samples (F = 0.055 ± 0.021; P < 0.001). Though highly significant (P < 0.001), heterozygote deficiency within populations relative to total population was moderate (F = 0.046 ± 0.016), suggesting a higher diversity within the populations (95.4%) than between populations. Various genetic distance estimation methods produced a similar topology of un-rooted dendrograms that grouped the overall Ethiopian donkeys into lowland (Ogaden, Omo and Sinnar) and highland (Abyssinian, Afar and Hararghe) genetic lineages. Likewise, Bayesian clustering analysis produced a similar pattern of clustering that was highly concordant with traditional donkey classification systems in Ethiopia.
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Publication Date: 2021-05-20 PubMed ID: 34018049DOI: 10.1007/s11250-021-02776-2Google Scholar: Lookup
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Summary

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This study explores the genetic diversity and structure of six separate Ethiopian donkey populations using equine microsatellite markers. The findings show a significant genetic variation within the populations rather than between them, and it also demonstrates that these populations can be grouped into lowland and highland genetic lineages.

Genetic Diversity Investigation

  • The researchers examined six different Ethiopian donkey populations: Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI).
  • To do this, they collected blood samples from 180 donkeys, making sure none of them were related. That means 30 samples were taken from each population’s donkeys.
  • They used 12 equine microsatellite markers to assess the genetic diversity and population genetic structure. These markers are sections of DNA that have sequences that repeat. They are used to determine genetic diversity because they often vary greatly among individuals.

Population Genetic Diversity Estimates

  • The results showed that a total of 94 alleles were found with a mean number of observed alleles of 5.208 ± 0.0229.
  • The average observed heterozygosity was 0.555 ± 0.023, indicating a fair amount of genetic diversity, and the expected heterozygosity was 0.588 ± 0.022.
  • There was a deficiency in heterozygote within the overall samples which was highly significant (F = 0.055 ± 0.021; P < 0.001). This means they found fewer heterozygotes than expected.

Population Genetic Structure

  • Although there was a moderate heterozygote deficiency within populations relative to the total population (F = 0.046 ± 0.016), it was highly significant. This suggests that there was higher diversity within donkey populations (95.4%) than between them.
  • When the genetic distances were estimated using various methods, a similar pattern emerged, dividing the Ethiopian donkeys into two genetic lineages: lowland (comprising Ogaden, Omo and Sinnar) and highland (Abyssinian, Afar and Hararghe).
  • This division was corroborated by Bayesian clustering analysis, a statistical method to infer population structure.
  • The clustering was in line with traditional donkey classification systems in Ethiopia.

This research indicates a considerably rich genetic diversity within rather than between the examined Ethiopian donkey populations. The findings give weight to the traditional classification methods and could have implications for the conservation of these animals.

Cite This Article

APA
Kefena E, Rosenbom S, Beja-Pereira A, Kurtu MY, Han JL, Dessie T. (2021). Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers. Trop Anim Health Prod, 53(3), 334. https://doi.org/10.1007/s11250-021-02776-2

Publication

Tropical animal health and production
ISSN: 1573-7438
NlmUniqueID: 1277355
Country: United States
Language: English
Volume: 53
Issue: 3
Pages: 334

Researcher Affiliations

Kefena, E
  • Department of Animal Genetics and Breeding, Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia. kefenaol@yahoo.com.
Rosenbom, S
  • Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal.
Beja-Pereira, A
  • Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal.
  • Department of Geosciences, Environment and Spatial Planning (DGAOT), Faculty of Sciences, University of Porto, Rua Campo Alegre 687, 4169-007, Porto, Portugal.
Kurtu, M Yusuf
  • Department of Animal and Range Sciences, Haramaya University, P.O. Box 38, Dire Dawa, Ethiopia.
Han, J L
  • CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China.
  • Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia.
Dessie, T
  • Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia.

MeSH Terms

  • Animals
  • Bayes Theorem
  • Equidae / genetics
  • Ethiopia
  • Genetic Variation
  • Genetics, Population
  • Horses / genetics
  • Microsatellite Repeats
  • Phylogeny

Grant Funding

  • PTDC/BIA-BDE/64111/2006 / Portuguese Foundation for Science (FCT)
  • Unknown / German Academic Exchange Service (DAAD)

References

This article includes 37 references
  1. Aranguren-Mendez J, Jordana J, Gomez M. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers. Genetics Selection Evolution 33, 433-442.
    doi: 10.1186/1297-9686-33-4-433google scholar: lookup
  2. Beja-Pereira A, England PR, Ferrand N, Jordan S, Bakhiet AO, Abdalla MA, Mashkour M, Jordana J, Taberlet P, Luikart G. African origin of domestic donkey. Science 304, 1781.
    doi: 10.1126/science.1096008google scholar: lookup
  3. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. .
  4. Blench RM. A history of donkeys, wild asses and mules in Africa. In: Blench RM, MacDonald KC (eds.), The origin and development of African livestock: archaeology, genetics, linguistics and ethnography. UCL Press, pp: 339–354.
  5. Bren M, Downs P, Irvin Z, Bell K. Intrageneric amplification of horse microsatellite markes with emphasis on the Przewalski’s horse (E. przewalski). Animal Genetics 25, 401-405.
    doi: 10.1111/j.1365-2052.1994.tb00530.xgoogle scholar: lookup
  6. Bren M, Downs P, Irvin Z, Bell K. Six equine dinuleotide repeats: microsatellites MPZ002, 3, 4, 5, 6 and 7. Animal Genetics 25, 124.
    doi: 10.1111/j.1365-2052.1994.tb00097.xgoogle scholar: lookup
  7. Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359-361.
    doi: 10.1007/s12686-011-9548-7google scholar: lookup
  8. Evanno G, Regnau TS, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Evolution 14, 2611-2620.
  9. Felsenstein J. PHYLIP (phylogeny inference package). Version 3.66. Seattle (WA): Genomes Sciences, Department of Genetics. University of Washington Software available from http://evolution.genetics.washington.edu/phylip.html.
  10. Guo SW, Thompson EA. Performing the exact test of Hardy–Weinberg proportions for multiple alleles. Biometrics 48, 361-372.
    doi: 10.2307/2532296google scholar: lookup
  11. Ishida N, Oyunsuren T, Mashima S, Mukoyama H, Saitou N. Mitochondrial DNA sequences of various species of the genus Equus with special reference to the phylogenetic relationship between Przewalskii’s wild horse and domestic horse. Journal of Molecular Evolution 41, 180-188.
    doi: 10.1007/BF00170671google scholar: lookup
  12. Ivankovic A, Kavar T, Caput P, Mioc B, Pavic V, Dovc P. Genetic diversity of three donkey populations in the Croatian costal region. Animal Genetics 33, 169-177.
    doi: 10.1046/j.1365-2052.2002.00879.xgoogle scholar: lookup
  13. Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801-1806.
    doi: 10.1093/bioinformatics/btm233google scholar: lookup
  14. Jordana J, Folch P, Aranguren JA. Microsatellite analysis of genetic diversity in the Catalonian donkey breed. Journal of Animal Breeding and Genetics 118, 57-63.
    doi: 10.1046/j.1439-0388.2001.00266.xgoogle scholar: lookup
  15. Kefena E, Beja-Pereira A, Han JL, Haile A, Mohammed YK, Dessie T. Eco-geographical structuring and morphological diversities in Ethiopian donkey populations. Livestock Science 141, 232-241.
    doi: 10.1016/j.livsci.2011.06.011google scholar: lookup
  16. Kefena E, Rosenbom S, Han J, Dessie T, Beja-Pereira B. Genetic diversities and historical dynamics of native Ethiopian horse populations (Equus caballus) inferred from mitochondrial DNA polymorphisms. Genes 12, 155.
    doi: 10.3390/genes12020155google scholar: lookup
  17. Kimura B, Marshall F, Chen S, Rosenbom S, Moehlman PD, Tuross N, Sabin RC, Peters J, Barich B, Yohannes H, Kebede F, Teclai R, Beja-Pereira A, Mulligan CJ. Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication. Proceeding of the Royal Society of Biological Sciences 278, 50-57.
    doi: 10.1098/rspb.2010.0708google scholar: lookup
  18. Langella O. Populations version 1.2.30. Available at: http://bioinformatics.org/~tryphon/populations/.
  19. Lei CZ, Ge QL, Zhang HC, Liu RY, Zhang W, Jiang YQ, Dang RH, Zheng HL, Hou WT, Chen H. African maternal origin and genetic diversity of Chinese domestic donkeys. Asian-Australian Journal of Animal Sciences 20(5), 645-652.
    doi: 10.5713/ajas.2007.645google scholar: lookup
  20. Lopez Lopez C, Alonso R, de Aluja AS. Study of the genetic origin of the Mexican Creole donkey (Equus asinus) by means of the analysis of the D-loop region of mitochondrial DNA. Tropical Animal Health and Production 37, 173-188.
    doi: 10.1007/s11250-005-9001-6google scholar: lookup
  21. Luikart G, Allendorf FW, Cornuet JM, Sherwin WB. Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity 89, 238-247.
  22. Marshall F. African pastoral perspectives on domestication of the donkey: A first synthesis. In: Denham TP, Jriarte J, Vrydaghs L (eds.), Rethinking agriculture: archaeological and ethno archaeological perspectives, One World Archaeology Series, Walnut Creek, CA, Left Coast Press. pp: 371-407.
  23. Moehlman PD. Status and action plan for the African wild ass. In: Moehlman PD (eds.), Equids: Zebras, Asses and Horses, Status Survey and Conservation Action Plan, IUCN, Gland, Switzerland. pp: 2-9.
  24. Nei M. Molecular Evolutionary Genetics. Columbia University Press, New York, USA.
    doi: 10.7312/nei-92038google scholar: lookup
  25. Nei M, Tajima F, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution 19, 153-170.
    doi: 10.1007/BF02300753google scholar: lookup
  26. Page RDM. TREEVIEW: an application to display phylogenetic trees on personal computers. Compendium of Applied Biosciences 12, 357-358.
  27. Peakall R, Smouse PE. GENALEX 6.41: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295.
    doi: 10.1111/j.1471-8286.2005.01155.xgoogle scholar: lookup
  28. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
    doi: 10.1093/genetics/155.2.945google scholar: lookup
  29. Raymond M, Rousset F. GENEPOP (version 3.3): Population genetics software for exact tests and ecumenicism. Journal of Heredity 86, 248-249.
    doi: 10.1093/oxfordjournals.jhered.a111573google scholar: lookup
  30. Reynolds J, Weir BS, Cokerham C. Estimation of the co-ancestry coefficients: basis for a short-term genetic distance. Genetics 105,767-79.
    doi: 10.1093/genetics/105.3.767google scholar: lookup
  31. Rosenberg NA. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes 4, 137-138.
    doi: 10.1046/j.1471-8286.2003.00566.xgoogle scholar: lookup
  32. Rosenbom R, Costa V, Al-Araimi N, Kefena E, Abdel-Moneim AS, Abdalla MA, Bakhiet A, Beja-Pereira A. Genetic diversity of donkey populations from the putative centers of domestication. Animal Genetics 46, 30-36.
    doi: 10.1111/age.12256google scholar: lookup
  33. Rossel S, Marshall F, Peters J, Pilgram T, Adams MD, O’Connor D. Domestication of the donkey: timing, processes and indicators. Proceedings of the National Academy of Sciences 105, 3715-3720.
  34. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Ecology and Evolution 4, 406-425.
  35. Watson M. Draft report on the African wild ass. Arusha, Tanzania. 5pp.
  36. Weir BS, Cockerham CC. ESTIMATING F-STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE.. Evolution 1984 Nov;38(6):1358-1370.
    pubmed: 28563791doi: 10.1111/j.1558-5646.1984.tb05657.xgoogle scholar: lookup
  37. Xu X, Gullberg A, Arnason U. The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs. Journal of Molecular Evolution 43, 438-446.
    doi: 10.1007/BF02337515google scholar: lookup

Citations

This article has been cited 2 times.
  1. Wang T, Liu Z, Shi X, Zhang Z, Li Y, Huang B, Ren W, Wang X, Wang C, Chai W. An investigation of genetic diversity in three Dezhou donkey original breeding farms.. Sci Rep 2023 Jul 11;13(1):11203.
    doi: 10.1038/s41598-023-38219-1pubmed: 37433834google scholar: lookup
  2. Wang Y, Hua X, Shi X, Wang C. Origin, Evolution, and Research Development of Donkeys.. Genes (Basel) 2022 Oct 25;13(11).
    doi: 10.3390/genes13111945pubmed: 36360182google scholar: lookup
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